Damn.

I don't know a lot about programming, but I can't help but feel like if we could abandon quests and restart them that a lot of these bugs could be avoided or circumvented.

Now there is a sensible suggestion, buckom! A lot of other games let you drop quests and then start them over, I wonder why Bethesda never thought of it? Maybe people will then come back and cry, it breaks immersion! If I make a decision in real life, I can't take it back in most situations! LOL
Anyway, I did the Transmundane quest on 4 characters and never had any issues. I guess, I usually just go and look for Septimus' outpost when I'm level 20 or over. My first character stumbled over it by accident, while out exploring the icy wastes. LOL
So, unfortunately for the OP, the only solution is to do it again on another toon, I guess.
